title: HDAC6 regulates NF-κB signalling by HDAC-dependent and independent mechanisms to control chondrocyte IL-1-induced MMP and inflammatory gene expression

status: Public on Oct 29 2021

city: Newcastle upon Tyne

first: Matt

last: Barter

address: International Centre For Life

country: United Kingdom

institute: Newcastle University

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Expression factors for oxalate stimulation in HEK293T cells

city: Sinjuku-ku

first: Hidekazu

last: Sugiura

state: Tokyo

address: Kawada-cho 8-1

country: Japan

institute: Tokyo Women’s Medical University

summary: parental HEK293T were challenged with 1064 µg/cm2 calcium oxalate monohydrate (COM) or sodium oxalate (NaOx) 4mM or vehicle for 24 hours and DNA microarray was performed.  We observed and selected two-fold upregulation of laminin, beta 3 (LAMB3), early growth response 1 (EGR1), gremlin 1, DAN family BMP antagonist, Ca++-dependent secretion activator 2, Ras association domain family member 3, interleukin 33 and bone morphogenetic protein 8a , and two-fold down-regulation of interleukin 37 and intercellular adhesion molecule 1 in COM lord compared to vhicle.

overall_design: parental HEK293T were challenged with 1064 µg/cm2 calcium oxalate monohydrate (COM) or sodium oxalate (NaOx) 4mM or vehicle for 24 hours.Total RNA was isolated from cells using RNeasy Plus Mini Kit (QIAGEN) and subjected to microarray data collection at Agilent Technologies Japan, Ltd. (Tokyo Japan) under following conditions.We compared the COM load sample (SAMPLE2; AR3085＿02) with the vhicle sample(SAMPLE1; AR3085＿01).


title: Biopsy-based single cell transcriptomics reveals MAIT cells as potential targets for controlling fibrosis-related liver inflammation due to chronic hepatitis-B infection

status: Public on Oct 28 2021

city: HangZhou

first: Li

last: Shao

state: None Selected

address: YuHangTang Road

country: China

institute: 杭州师范大学

type: Expression profiling by high throughput sequencing

summary: We profiled the transcriptomes of about 2,4000 single cells from biopsied liver tissues from six chronic HBV patients with different grades of liver inflammation.

overall_design: Examination of the single cells along liver inflammation progression

first: Xiaohui

last: Fan


title: Distinct transcriptional signatures in mIDH leukemia cells as compared to wild type

status: Public on Oct 30 2021

city: Nashville

first: Paul

middle: Brent

last: Ferrell

state: TN

address: 777 Preston Research Bldg., 2220 Pierce Ave.

department: Medicine

country: USA

institute: Vanderbilt University Medical Center

summary: We report the results of bulk RNA sequencing on both parental and mIDH2R140Q TF-1 cell lines. We obtained 1 million cells of each cell line and extracted RNA to generate libraries. Our sequencing was performed with Novogene assistance. Differentially expressed genes (DEGs) were analyzed using DEseq2. Ultimately, we compared the expression of NF-κB targets and our results indicated upregulation of IL-1, IFNα and IFNγ in the mIDH2 cell line as compared to parental. Additionally using GSEA software, we noted increased expression of upstream and downstream constituents of the NF-κB pathway. This component of our study indicates the broad transcriptional changes induced by mIDH2R140Q mutation and demonstrates the upregulation of NF-κB specifically.

overall_design: Examination of impact of mIDH2R140Q mutation in TF-1 leukemia cell lines

first: Kathryn

middle: I

last: Sunthankar

middle: B


title: The c-Rel transcription factor limits early interferon and neuroinflammatory responses to prevent herpes simplex encephalitis onset in mice

city: Montreal

first: Silvia

middle: M

last: Vidal

state: Quebec

address: 3649 Promenade Sir-William-Osler

department: Human Genetics

country: Canada

institute: McGill University

summary: c-Rel is a transcription factor and a subunit of NF-kΒ encoded by the Rel gene. We previously demonstrated that a truncating cysteine to stop codon mutation at amino acid position 307 of c-Rel (RelC307X) results in susceptibility to herpes simplex virus type 1 (HSV-1). Approximately 60% of mutant RelC307X mice succumb to lethal herpes simplex encephalitis (HSE) in the hindbrain between days 6 and 9 postinfection, compared to resistant wild-type (Rel+/+) controls. Here, we performed dual host-pathogen RNA sequencing on Rel+/+ and RelC307X brainstems to measure differential viral and host gene expression that may underlie HSE susceptibility in mutant mice. Briefly, brainstems were harvested from Rel+/+ and RelC307X mice prior to HSE symptom onset at day 5 post-HSV-1 infection, compared to brainstems collected from non-infected control mice. Total RNA was isolated from bulk tissue using TRIzol (Invitrogen) and further column-purified using the RNeasy Mini Kit (Qiagen). RNA quality was assessed using Bioanalyzer RNA Pico chips (Agilent), and libraries were prepared following rRNA depletion. Libraries were sequenced on an Illumina HiSeq 2500 sequencer in paired-end 50bp configuration. Sequencing reads were aligned to both mouse and HSV-1 strain 17 reference genomes to obtain both host and viral gene expression counts. In total, 5 Rel+/+ and 6 RelC307X brainstem samples were analyzed at day 5 post-infection, and 4 Rel+/+ and 4 RelC307X independent non-infected samples as controls. Day 5 HSV-1-infected samples were further subdivided into high- or low-responder within both genotype groups based in part on the level of viral and host defence gene expression in each sample.

overall_design: Dual host-virus RNA sequencing was performed on bulk brainstem tissue to generate mRNA gene expression profiles of adult female wild-type (Rel+/+) and mutant (RelC307X) mice following intranasal HSV-1 infection, compared to non-infected control mice. HSV-1 infected mice are divided into high- and low-responders to HSV-1 infection.

first: Mathieu

last: Mancini

first: Benoît

last: Charbonneau

first: David

last: Langlais


title: Dynamic network biomarker analysis discovers IbNAC083 in initiation and regulation of sweet potato root tuberization

status: Public on Oct 31 2021

city: Shanghai

first: Shutao

last: He

address: 320 Yue Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

summary: The formation and development of storage roots is an intricate process regulated via a complex transcriptional regulatory network. To significantly advance our understanding of the molecular mechanisms governing storage root initiation and development in sweet potato, we performed a comprehensive analysis of transcriptome dynamics during root development.

overall_design: Root mRNA profiles of sweet potao at seven different developmental stages

first: Xiaomeng

last: Hao

first: Luonan

last: Chen

first: Peng

last: Zhang


title: GFI1 and IKAROS

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing


title: A comprehensive analysis of metabolomics and transcriptomics reveals a novel crizotinib resistance mechanism in non-small cell lung cancer

city: Zhengzhou

first: Yueqin

last: Wang

address: No.1 Jianshedong Rd

institute: Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University

summary: Crizotinib is a first-line targeted therapy against EML4-ALK fusion in non-small cell lung cancer (NSCLC), but the increased resistance limits its clinical application. However, the mechanisms underlying such resistance are largely unexplored. The present study identified ALK protein overexpression in crizotinib-resistant H3122CR cells through immunoblotting. Then, liquid chromatography tandem mass spectrometry-based metabolomics was adopted to investigate metabolic responses. Crizotinib resistance was associated with the reduction of the total lipid content and the increase of organic acid, featuring the upregulation of lipid metabolism. Fatty acid β-oxidation pathway reprogrammed crizotinib-sensitive metabolome to crizotinib-resistant metabolome, resulting in crizotinib resistance. These findings reveal a previously unknown mechanism of crizotinib resistance and suggest promising applications of this approach in prognostic prediction and tailored therapeutics of NSCLC patients.

overall_design: mRNA profiles of H3122 and H3122 crizotinib-resistant cells

first: Luyao

last: Feng

first: Shaoxuan

last: Zhou

first: Yu

first: Xin

last: Tian

first: Jing

last: Yao

first: Yingjie

last: Xu


title: ASIC3-M-CSF-M2 macrophage-positive feedback loop modulates in skin fibrosis pathogenesis

city: wuxi

first: Siyu

last: Liu

address: Street of River Deans, Binhu District, Wuxi City

institute: Jiangnan University Affiliated Hospital

summary: Inflammation is one of the main pathological features leading to skin fibrosis and a key factor leading to the progression of skin fibrosis. Acidosis caused by a decrease in extracellular pH is a sign of the inflammatory process. Acid-sensing ion channels (ASICs) are ligand-gated ion channels on the cell membrane that sense the drop in extracellular pH. However, the molecular mechanisms by which skin fibroblasts are regulated by Acid-sensing ion channel 3(ASIC3) remain unknown. This study investigated whether ASIC3 is related to inflammation and skin fibrosis and explored the underlying mechanisms. We demonstrate that Macrophage colony-stimulating factor (M-CSF) is a direct target of ASIC3, and ASIC3 activation promotes M-CSF transcriptional regulation of macrophages for M2 polarization. The polarization of M2 macrophages transduced by the ASIC3-M-CSF signal promotes the differentiation of fibroblasts into myofibroblasts through transforming growth factor β1 (TGF-β1), thereby producing ASIC3-M-CSF-TGF-β1 positive feedback loop. Targeting ASIC3 may be a new treatment strategy for skin fibrosis.

first: Junjie

last: Wu

first: Fenglai

last: Yuan


title: Transcriptomic profiling of simvastatin-treated human umbilical vein endothelial cells

city: Boston

first: Johannes

last: Wedel

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: We report that simvastatin induces an immunoregulatory transcriptional profile in endothelial cells that is potent to modulate CD4+ T cell biology.

overall_design: Human umbilical vein endothelial cells were cultutred in presence of 1 or 10 µM simvastatin or vehicle for 24 hours (duplicate conditions). Total RNA was isolated and RNA-seq libraries were prepared using 8-bp barcodes with standard Illumina adaptors.

first: Sek

middle: W

last: Kong

first: Timna

last: Agur

last: Briscoe


title: RNA sequencing of Opa1-silenced HUVECs.

city: Padova

first: Stephanie

last: Herkenne

state: Veneto

address: Via Ugo Bassi

department: Biology

country: Italy

institute: University of Padova

summary: The goal of this study is to compare the transcriptome of HUVECs silenced or not for Opa1

overall_design: To investigate the effect of Opa1 silencing on the transcriptome of endothelial cells.

first: L

last: Scorrano

first: S


title: Increased ACTL6A Occupancy Within mSWI/SNF Chromatin Remodelers Drives Human Squamous Cell Carcinoma

city: Stanford

first: Zohar

last: Shipony

state: CA

address: Beckman Center B-279A  279 Campus Drive West

institute: Stanford University


title: Therapeutic Interrupting C/EBPβ-Clec7a Cross-talk-mediated NLRP3 Inflammasome-dependent Pyroptosis for Relieving Neuropathic Pain

city: Beijing

first: Dan

address: No. 16, Nei Nanxiao Street, Dongzhimen, Dongcheng District

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

summary: Neuropathic pain (NP) is a complex chronic pain due to the nervous system damage or diseases.During NP development and progression, the neuroinflammation has been observed along the pain pathways from the spinal cord to the thalamus and the parietal cortex. It may be caused by the activation of glial cells, especially microglia, with production of cytokines and other inflammatory mediators within the central nervous system (CNS), especially in spinal cord. In this study, we used high-throughput RNA-seq technology to detect the global gene expression in spinal cord of rats in sham group and CCI model group(an animal model of neuropathic pain), and the differentially expressed genes between diseases and control group were obtained.Significant differentially expressed genes (DEGs) of the Sham vs. CCI groups were identified using the criteria of a fold change>1.5 and P value <0.05. Finally, we focused on C/EBPβ-Clec7a Cross-talk-mediated NLRP3 Inflammasome-dependent Pyroptosis pathway and further studied its role in neuropathic pain.

overall_design: SC tissues (L4-L6) collected from the rats in the Sham and CCI groups (n=4 per group) on postoperative day 10 were immersed in TRIzol (Invitrogen, CA, USA) and immediately frozen in liquid nitrogen for the detection.Sequencing libraries were generated using NEBNextUltra RNA Library Prep Set for Illumina (NEB, USA.). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia). After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform. Gene expression profiling was analyzed using R (http://www.rproject.org/, version 3.1.1) with Bioconductor packages (http://www.bioconductor.org/). Raw intensities were normalized using Robust multi-array average (RMA method).

first: Chunhui

last: Zhao

first: Haiyu

first: Yanqiong

last: Zhang


title: Expression of tRF & tiRNA in cholangiocarcinoma by RNA sequencing

city: Shenyang

first: Bengang

last: Wang

address: North Nanjing Street 155#

institute: China Medical University

summary: The rapid development of high-throughput sequencing is conducive to the discovery of many new theories. The purpose of this study is to explore the differentially expressed of tRF & tiRNA in cholangiocarcinoma by high-throughput sequencing technology. We collected cholangiocarcinoma and adjacent normal tissues from three patients. After RNA extraction and RNA library preparation, we  determined the raw data of tRF & tiRNA in cholangiocarcinoma and adjacent normal tissues by high-throughput RNA sequencing. Raw data were generated after sequencing,image analysis,basecalling and quality filtering on lllumina sequencer.Firstly,Q30 was used to perform quality control.The adaptor sequences were trimmed and the adaptor-trimmed-reads(>=16nt) were left by cut adapt software(v1.9.3).Then,the raw counts of each tRF&tiRNA(MINTbasev2.0) was calculated for all samples,defined as the raw expression level soft.The results showed that a total of 20102 tsRNA were detected in the two groups, 9616tsRNA were upregulated and 10486 were downregulated. There were 535 differentially expressed tsRNA  in cholangiocarcinoma after edger standardization, of which 241 were upregulated and 294 were downregulated (| log2 (foldchange) | = 1andpvalue < 0.05). This study shows that high-throughput sequencing technology is helpful for us to determine the expression of tRF & tiRNA in cholangiocarcinoma, and to screen out differentially expressed tRF & tiRNA, and further to explore the factors that affect the progress of cholangiocarcinoma.

overall_design: Examing 2 conditions, each with 3 replicates

first: Ben-gang

first: Qian


title: The 40S-LARP1 complex reprograms the cellular translatome upon mTOR inhibition to preserve the protein synthetic capacity

city: L'Hospitalet de Llobregat

first: Antonio

last: Gentilella

state: Barcelona

address: granvia de l'Hospitalet, 199

department: ONCOBELL

country: Spain

institute: IDIBELL

summary: Ribosomes execute the transcriptional program in every cell. Critical to sustain nearly all cellular activities, ribosome biogenesis requires the translation of ~200 factors of which 80 are ribosomal proteins (RPs). As ribosome synthesis depends on RP mRNAs translation, a priority within the translatome architecture should exist to ensure the preservation of ribosome biogenesis capacity, particularly under adverse growth conditions. Here we show that under critical metabolic constraints characterized by mTOR inhibition, LARP1 complexed with the 40S subunit protects from ribophagy the mRNAs regulon for ribosome biogenesis and protein synthesis, acutely preparing the translatome to promptly resume ribosomes production after growth conditions return permissive. Characterizing the LARP1-protected translatome revealed a set of 5’TOP transcript isoforms other than RPs involved in energy production and in mitochondrial function, among other processes, indicating that the mTOR-LARP1-5’TOP axis acts at the translational level as a primary guardian of the cellular anabolic capacity

overall_design: Sucrose fractionation of polysomal lysates from parental or LARP1 KO  cells treated with TAK228 for 48 hours (TORi replicates r1 and r2). Non-polysomal protected translatome was analyzed

first: Virginia

last: Diez-Obrero


title: Genome-wide identification of genes directly regualted by GFI1 and IKAROS in CCRF-CEM cells

first: Jingtao

last: Guo

summary: To study the interplay between GFI1 and IKAROS in T-cell Acute Lymphoblastic Leukemia (T-ALL), we applied ChIP-Seq to CCRF-CEM cells expressing 3XFLAG-tagged GFI1 OR IKAROS under doxycycline-inducible control.We found these two protiens associated with common genes, including genes associated with T cell development.

overall_design: Examine GFI1 and IKAROS binding genes in CCRF-CEM cells

first: Wenxiang

last: Sun

first: Michael

middle: E

last: Engel

first: Dean

last: Tantin


title: RNA sequencing reveals particulate matter exposure-induced cholesterol metabolism disorder in ferret lung epithelial cells

city: Kaifeng

first: Haigang

last: wu

state: Henan province

address: dongjing Road

department: School of Life Sciences

institute: Henan University

summary: We report the biological effect of particulate matter on ferret lung epithelial cells with different concentration 500 ug/mL and 250 ug/mL. Treatment time is 48 h.

overall_design: Examination of transcriptome levels in ferret lung epithelial cells treated with particulate matter.

last: Wu

first: Ting

last: Yin


title: The role of long noncoding RNA EGFR-AS1 in cancer

city: Singapore

first: Azhar

last: Ali

address: 14 Medical Drive MD6 #11-01

department: CSI Singapore

country: Singapore

institute: National University of Singapore

summary: Expression of long noncoding RNA EGFR-AS1 is found to be dysregulated in cancer especially non small cell lung cancer. However, the role of long noncoding RNA EGFR-AS1 in non small cell lung cancer remains relatively unknown. Our study aim to discovered the role of long noncoding RNA EGFR-AS1 in lung cancer progression and response to chemotherapy.

overall_design: Long noncoding RNA EGFR-AS1 is overexpressed stably in the NCI-H1703 cells. RNA expression in the EGFR-AS1 overexpressed NCI-H1703 is profiled by RNA-seq and compared with vector transfected NCI-H1703.

first: Chee

last: Fhu

first: Jun

middle: T

last: Teo


title: RNA sequencing of whole blood cells in patients with trigeminal neuralgia

first: Yi

last: Feng

address: No.11,Xizhimen South Street, Xicheng District

department: Department of Anesthesiology

institute: Peking university people's hospital

summary: Trigeminal neuralgia (TN) is a type of neuropathic pain caused by injury to sensory nerves, manifesting as severe paroxysmal pain of the head and face. Trigeminal neuralgia brings a huge burden to patients, without long-term effective treatment. Changes in the expression of pain-related genes in the whole blood samples of patients play an important role in the pathogenesis, diagnosis, and evaluation of treatment effects of trigeminal neuralgia. To better understand the mechanism of trigeminal neuralgia, we collect the whole blood samples from the trigeminal neuralgia patients and the pain-free healthy comparisons. RNA-seq was conducted between the two groups to find the transcriptome changes in patients with trigeminal neuralgia.

overall_design: Whole blood samples were collected from the trigeminal neuralgia patients and healthy pain-free controls, (n = 10).

first: Chao

last: Xu


title: LARP7 ameliorates cellular senescence and aging-related atherosclerosis by allosterically enhancing SIRT1 deacetylase activity

city: Minhang

first: bing

last: zhang

state: Shanghai

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

summary: Cell senescence is a cell state characterized with permanent cell cycle arrest and elevated proinflammatory secretome and associated with pleiotropic essential physiopathological processes. The persistent DNA damage response (DDR) is the major stress leading to senescence, however the molecular mechanism underling remains elusive. Here, we identified the La Ribonucleoprotein 7 (LARP7), a 7SK RNA binding protein, as a novel SIRT1 deacetylase activator. It directly interacted with SIRT1 allosteric regulatory domain and enhanced its deacetylase activity. DDR-mediated ATM activation trigged the extracellular shuttling and downregulation of LARP7 that dampened the SIRT1 deacetylase activity and enhanced p53 and NFB (p65) transcriptional activity by augmenting their acetylation. As a consequence, activated p53 and NFB arrested cell growth and promoted SASP genes expression, and thereby accelerated the cellular senescence. Inducible deletion of LARP7 in wildtype mouse led to senescent cell accumulation and premature ageing. Furthermore, we identified that ATM-LARP7-SIRT1-p53/NFB senescent axis was active in the aortic senescence and atherogenesis. Genetic depletion of LARP7 aggravated the atherogenesis but conversely, inhibited ATM activation or restoring LARP7 expression with genetic manipulation alleviated the vascular aging and atherogenesis. Together, this study identifies LARP7 as a novel SIRT1 cellular activator and it’s-mediated ATM-LARP7-SIRT1-p53/NFB axis is attributed to DDR-mediated cellular senescence and aging-related pathologies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We used RNA-seq to profile and compare the transcriptome in wildtype and  LARP7-depleted IMR90 cells and MEFs.

first: Pengyi

last: Yan

first: Zixuan

last: li

first: Junhao

last: Xiong

first: Zilong

last: Geng

first: Weiting

last: Wei

first: Lizhen

first: Wei

last: Deng

first: Yan

first: Gengze

first: Tao

last: Zhuang

first: Xiaoyu

last: Tian

first: Ming

last: Lei

first: Yuzhen

first: William

last: Pu

first: Junling

last: Liu

first: Feng

last: Chen

first: Kun

first: Chunyu

last: Zeng

first: Yu

last: Huang

first: Bing


title: Genes relevant to tissue response to cancer therapy display diurnal variation in mRNA expression in human oral mucosa

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: We conducted RNA-seq assay on individual oral mucosal samples collected from 11 healthy volunteers every 4 hours (6 time points). Using a cosine-based method, we estimated the individual and average values of peak-time and amplitude for each gene. Correlations between gene expression peak-times and age was examined, adjusting for individual's sleep timing.

overall_design: 11 subjects. 6 samples per subject taken every 4 in a lapse of 24 hours

first: Fangyi

last: Gu

middle: C

last: Gomez

first: Jianhong

first: Matthew

middle: F

last: Buas

first: Nicolas

last: Schlecht

first: Karen

last: Hulme

first: Shweta

middle: V

last: Kulkarni

first: Prashant

middle: K

last: Singh

first: Richard

last: O'Connor

first: Christine

last: Ambrosone

first: Anurag

first: Jianmin

last: Wang


title: Transcriptome analysis of Plasmodium falciparum isolates from Benin reveals specific gene expression associated with cerebral malaria

city: Paris

first: Gwladys

last: Bertin

address: rue de l'observatoire

country: France

institute: Institut de Recherche pour le Développement

summary: The most severe form of Plasmodium falciparum infection, cerebral malaria (CM), is linked to the parasite’s ability to bind to specific endothelial receptors in brain capillaries. However, the host and parasitic factors causing CM are not yet fully elucidated and the transcriptome profile of P. falciparum isolated from patients with CM remains largely unknown. To complement this deficiency, we aimed to characterize the gene expression associated with CM, by sequencing the parasite’s transcriptome from 15 CM and 15 uncomplicated malaria Beninese children. We demonstrated a specific gene expression in CM, making it possible to completely distinguish the two clinical phenotypes. Numerous biological pathways including entry into host and cytoadherence were predicted as impacted. In addition, infected erythrocytes (iE) from CM children had a decreased circulation time. It may be the result of a stronger adhesion capacity of these iE, which we previously demonstrated in vitro. Consistent with this result, we were able to measure an overall increased expression of the var genes family, encoding for the major mediator of adherence to host endothelium. This phenomenon may allow iE to avoid splenic clearance and cause the increased parasitaemia measured in CM.

overall_design: RNA-seq data of P. falciparum isolates from CM and UM beninese children

first: Emilie

last: Guillochon

first: Jérémy

last: Fraering

first: Valentin

last: Joste

first: Claire

last: Kamaliddin

first: Bertin

last: Vianou

first: Ludivine

last: Houzé

first: Laura

middle: G

last: Baudrin

first: Jean-François

last: Faucher

first: Agnès

last: Aubouy

first: Sandrine

first: Michel

last: Cot

last: Argy

first: Olivier

last: Taboureau


title: LncRNA RP5-998N21.4 promotes immune defense through upregulation of IFIT2 and IFIT3 in schizophrenia

city: Guangzhou

first: Cunyou

last: Zhao

state: Guangdong

address: No. 1023-1063, South Sha-tai Road, Baiyun District

institute: Southern Medical University

summary: We recently identified a schizophrenia-associated upregulated long noncoding RNA (lncRNA) RP5-998N21.4 by transcriptomic analysis of monozygotic twins discordant for schizophrenia. Importantly, we found that genes coexpressed with RP5-998N21.4 were enriched in immune defense-related biological processes in twin subjects and in RP5-998N21.4-overexpressing (OE) SK-N-SH cell lines. We then identified two genes encoding interferon-induced protein with tetratricopeptide repeat (IFIT) 2 and 3, which play an important role in immune defense, as potential targets of RP5-998N21.4 by integrative analysis of RP5-998N21.4OE-induced differentially expressed genes (DEGs) in SK-N-SH cells and RP5-998N21.4-coexpressed schizophrenia-associated DEGs from twin subjects. We further demonstrated that RP5-998N21.4 positively regulates the transcription of IFIT2 and IFIT3 by binding to their promoter regions and affecting their histone modifications. In addition, as a general nuclear coactivator, RMB14 (encoding RNA binding motif protein 14) was identified to facilitate the regulatory role of RP5-998N21.4 in IFIT2 and IFIT3 transcription.

overall_design: Total RNA were extracted from  RP5-998N21.4 overexpressed (n=2) or wild type (WT, n=2) SK-N-SH cells  and  performed by deep sequencing, using Illumina.

first: Bo

last: Guo

first: Tingyun

last: Jiang

first: Hongyu

last: Ni

first: Junping

last: Ye

first: Xiaohui

last: Wu

first: Chaoying

first: Meijun

first: Linyan

first: Zhongwei

last: Li

first: Xianzhen

last: Zheng

first: Shufen

first: Qiong

last: Yang

first: Zhongju


title: HDAC6 regulates NF-κB signalling by HDAC-dependent and independent mechanisms to control chondrocyte IL-1-induced MMP and inflammatory gene expression [HDAC siRNA exp]

city: Newcastle upon Tyne

first: Matt

last: Barter

address: International Centre For Life

institute: Newcastle University

summary: Analysis of the effect of HDAC6 knockdown on IL-1-induced gene expression in SW1353 chondrocytes.

overall_design: Total RNA obtained from SW1353 chondrocytes treated with HDAC6 or non-targetting siRNA prior to stimulation with IL-1alpha for 6 hours.

first: David

last: Young


title: Genes expression during stem growth of Populus alba x Populus tremula var. glandulosa

city: Hangzhou

first: weti

last: Lu

state: China

address: WUSUSTREET NO.666

institute: zhejiang A&F university

summary: To obtain genes expression in different parts of 84k poplar stems, transcriptome sequencing was performed using Illumina Novaseq 6000 second-generation sequencing platform from Shanghai BIOZERON Co. Ltd (www.biozeron.com). Selecte three stem segments of plants REPEAT 1, 2 and 3 with good and similar growth to use: 2nd-3rd internodes (poplar stem top: PST1, PST2, PST3); 9th-10th internodes (poplar stem middle: PSM1, PSM2, PSM3); 14th-15th internodes (poplar stem bottom: PSB1, PSB2, PSB3). [Or the three repeating organisms are also called poplar A, B, C. From top to bottom, the three parts of the stem are also called stem 1, 2, 3.]

overall_design: Genes expression of 84K poplar stems of top, middle and bottom

first: Weitai

first: Wei

last: Zeng


title: A long non-coding RNA in the let-7complex acting as a potent and specific death effector of cancer cells [IVT]

city: Basel

first: Tommy

middle: Beat

last: Schlumpf

state: Basel-Stadt

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

summary: The let-7 complex in Drosophila encodes three evolutionarily conserved microRNAs: miR-100, let-7, and miR-125. These act as heterochronic genes in regulating developmental timing in response to the steroid hormone ecdysone and play important roles in cell differentiation. Here we identify two additional long non-coding RNAs in the let-7 complex, we named let-A and let-B. Both are transcribed in the large first intron of the primary RNA encoding the microRNAs. We show these RNAs to be sequentially expressed in early pupal stages in response to ecdysone signaling, albeit exhibiting a different expression pattern compared to the microRNA let-7. Surprisingly, ectopic expression of let-A in Drosophila cancer cells induces rapid cell death. Dead cells further release RNA molecules in the medium that is becoming toxic to other cancer cells. In vivo grown tumors lose their tumorigenicity after being incubated in the let-A induced medium. Moreover, feeding flies carrying transplanted tumor cells with such induced medium leads to reduced growth of tumors in a subset of hosts. Our results uncover a new lncRNA which can act as a potent and specific cell death effector for Drosophila tumor cells.

overall_design: Determination of enrichment of let-A in vitro transcripts after exposure to cell extracts.

first: Tosca

last: Birbaumer

first: Makiko

last: Seimiya

first: Yanrui

first: Renato

last: Paro


title: HDAC6 regulates NF-κB signalling by HDAC-dependent and independent mechanisms to control chondrocyte IL-1-induced MMP and inflammatory gene expression [TSA exp]

summary: Analysis of the effect of HDAC inhibitor TSA on IL-1-induced gene expression in SW1353 chondrocytes.

overall_design: Total RNA obtained from SW1353 chondrocytes treated with TAA (250ng/ml) prior to stimulation with IL-1alpha for 6 hours.


title: Next Generarion sequencing identifing changes of gene expression mediated by ectopic GFI1 expression or CRISPR-mediated IKAROS knockout

city: Salt Lake City

first: Jingtao

address: 2000 Circle of Hope

institute: University of Utah School of Medicine

summary: To identify changes in gene expression associated with either ectopic GFI1 expression or CRISPR-mediated IKAROS knockout, we applied bulk RNA-Seq with GFI1-3XFLAG CCRF-CEM cells. Wild type or IKAROS knockout cells were treated with vehicle or doxycycline for 24 hours. Between 21.7 and 28.2 million RNA-Seq reads were generated for each condition, 88.6 to 90.3% of which aligned uniquely to the human Hg38 reference genome. ~99% of the reads within coding regions aligned to the correct strand. Hierarchically clustering the top 500 most significantly differentially regulated genes across all the conditions (ranked based on p-value) revealed groups of genes repressed and activated by the different manipulations.

overall_design: mRNA profiles of WT or IKAROS KO CCRF-CEM cells inducibly expressing GFI1(Doxycycline) or not (PBS)

first: Wenxiang

last: Sun

first: Michael

last: Engel

first: Dean

last: Tantin


title: Anti-cnacer effects of ginsenoside Rh2 with doxorubicin from breast tumor bearing mice

city: Daejeon

first: Yee-Jin

last: Yun

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: The FDA approved drug Doxorubicin provokes copious irreversible cardiotoxicity and even increases the risk of heart failure. Considering the multiple and interacted molecular pathways in cancer, there is a big possibility that tumors are simultaneously sensitive to different drugs. This makes achievable to study the combinations of drug, having the virtues of less toxicity, higher efficacy and potentially antagonizing drug resistance in cancer therapy. In the present study, we addressed the synergistic effects of ginsenoside Rh2 on doxorubicin-treated breast cancer bearing mice. We showed that Rh2 significantly enhanced the anti-cancer effects of doxorubicin and greatly attenuated the cardiotoxicity. Transcriptomic changes can clearly distinguish the chemotherapeutic groups and non-treated control groups. Transcriptomic analysis domestrated that Rh2 protection involved in multiple vital pathways including cellular stress, apoptosis and inflammation.

overall_design: Examination of pontential anti-cancer effects of ginsenoside Rh2 by analyzing transcriptomes changes between doxorubicin treated samples with or without ginsenoside Rh2 and vehicle samples.

first: Yeejin

first: Sunchang

last: Kim


title: Transcriptome analysis of Arabidopsis low molecular weight protein phosphatase mutant aph in response to Abscisic acid

city: shanghai

first: li

last: peng

institute: PSC

summary: We compared the the transcriptome of wild type and a knock-out mutant of Involvement of low molecular weight protein tyrosine phosphatase, aph-1, with or without ABA treatment in Arabidopsis

overall_design: two-week-old seedlings of Col-0 and aph-1 mutant, with and without 6 h ABA treatment

first: Yanyan

last: Du

first: Shaojun

last: Xie

first: Yu

last: Ma

first: Pengcheng

last: Wang


title: Synergistic hepatoprotective effect of the TLR5 agonist CBLB502 and its downstream effector IL-22

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

institute: University of Bern

summary: We have shown that CBLB502 (CBLB) display hepatoprotective activities, and triggers a strong IL-22 release. To understand the hepatoprotection, we describe the response of isolated adult mouse hepatocyte to IL-22, CBLB, or IL-22 + CBLB exposure.

overall_design: Primary mouse hepatocytes (C57BL/6) were isolated from livers of 3 donors. Plated mouse hepatocytes were then treated with 1ng/ml of IL-22, or 4ng/ml CBLB or the combination of the two (IL-22+CBLB) and incubated for 2hours before RNA extraction and RNA-seq.

first: Nicolas

last: Melin

last: Sánchez-Taltavull

first: Deborah

last: Stroka


title: Colorectal cancer

status: Public on Oct 27 2021

city: Chongqing

first: Bosheng

last: Li

address: Gaotanyan Street

institute: Army Medical University

summary: Colorectal cancer and colocrectal metasis

overall_design: CRC vs. CRLM tissues


title: TET deficiency promotes oncogenesis and DNA damage in B cells by increasing the levels of G-quadruplexes and R-loops [G4-seq]

city: La Jolla

first: Anjana

last: Rao

state: California

address: 9420 Athena Cir

department: Signaling and Gene Expression

institute: La Jolla Institute for Allergy and Immunology

summary: Enzymes of the TET family are methylcytosine dioxygenases that undergo frequent mutational or functional inactivation in both hematological and solid cancers. Recent studies have identified recurrent loss-of-function mutations in TET proteins in human patients with Diffuse Large B-Cell Lymphoma (DLBCL). Here we investigate the role of TET proteins in the pathogenesis of DLBCL by deleting the Tet2 and Tet3 genes in mature B cells in mice. Tet deletion perturbs mature B-cell homeostasis and causes spontaneous development of Germinal Center-derived B cell lymphomas. We show that an increase in G-quadruplexes and R-loops a common feature of TET deficiency in B cells as well as other hematopoietic cells. Genome-wide analyses revealed that G-quadruplexes and R-loops accumulated primarily near transcription start sites in TET-deficient B cells, and their accumulation correlated with increased DNA double-strand breaks. Moreover, CRISPR-mediated depletion of nucleases and helicases that regulate G-quadruplexes and R-loops led to decreased viability of TET-deficient but not control primary B cells. Our studies elucidate a molecular mechanism by which TET loss-of-function might predispose to development of B cell-derived and other malignancies, and highlight novel therapeutic avenues that could be further explored.

overall_design: G4-sequencing in CD19 Tet2/3 DKO B cells

first: Vipul

last: Shukla

first: Daniela

last: Samaniego-Castruita


title: microRNA expression data of tumor tissues and paired pericarcinomatous tissue of 15 ESCC samples

city: Shantou

first: Yang

last: Chen

address: Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou

institute: Shantou University Medical College

summary: We detected the expression of miRNA in 15 ESCC samples' tumor tissues and the corresponding normal esophagus tissue. Then, we identified the differentially expressed miRNAs in ESCC.

overall_design: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat#5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section. Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent  technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings. Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

first: Qian

last: Yang

first: En-Min

first: Li-Yan

last: Xu


title: Neuron-derived exosome from plasma show altered miRNA cargo as a function of antidepressant drug response.

city: Montreal

first: Gustavo

last: Turecki

address: 6875 Boulevard LaSalle

department: Psychiatry

institute: McGill University

type: Non-coding RNA profiling by high throughput sequencing

summary: We investigated NDEs from depressed and psychiatrically healthy controls, before and after, eight weeks of antidepressant treatment (ADT).  Neuronal-derived exosomes contained miRNA that showed enrichment for brain functions. Changes in NDE cargo, specifically miR-21-5p, miR-30d-5p, and miR-486-5p expression, were significantly associated with ADT response. Furthermore, we found these targets to be altered in brain tissue from depressed individuals. Together, our study indicates that changes in peripherally isolated NDE can act as a biomarker of ADT response specifically through size and cargo.

overall_design: MiRNA cargo of neuronal-derived  exosomes from 40 MDD patients, half of which responded to antidepressant treatment, and half of which did not. In addition, 20 psychiatrically healthy controls were used. Data is included from exosomes extracted both before and after treatment.

first: Saumeh

last: Saeedi

first: Corina

last: Nagy

first: Jean-Francois

last: Theroux

first: Laura

last: Fiori

first: Pascale

last: Ibrahim

first: Jennie

first: Marina

last: Wakid

first: Susan

last: Rotzinger

first: Jane

middle: A

last: Foster

first: Naguib

last: Mechawar

first: Sidney

middle: H

last: Kennedy


title: Autophagy protects integrity of tumor suppressors from replication stress

city: Nagasaki city

first: Tsuyoshi

last: Kawabata

state: Nagasaki

address: 1-12-4 Sakamoto

department: Atomic Bomb Disease Institute

institute: Nagasaki University

summary: To understand the changes in gene expression in autophagy-deficient cells after the exposure to endogenous or exogenous replication stress, we carried out whole-genome microarray expression profiling of untreated and aphidicolin-treated ATG7-/- HEK293 cells.

overall_design: Gene expression profile of ATG7-/- HEK293 cells was measured at 2 weeks recovery culture after treatment with 300nM aphidicolin for 3 days.


title: Angiotensin II-induced long non-coding RNA Alivec regulates chondrogenesis in vascular smooth muscle cells

city: Duarte

first: Rama

last: Natarajan

address: 1500 E Duarte Rd

department: Department of Diabetes Complications and Metabolism

institute: Beckman Research Institute, City of Hope

summary:
Alivec is a novel lncRNA found to be upregulated by Ang II stimulation in rat vascular smooth muscle cells (RVSMCs). The regulatory mechanisms of rat Alivec have not been reported so far.
We used microarrays to investigate Alivec-mediated global gene expression and identified distinct classes of up- and down-regulated genes.

overall_design: RVSMCs were isolated from male Sprague-Dawley rats by enzymatic digestion and cultured for 3 passages before using in experiments. Cells were transfected with either negative control GapmeR (NCGap) or  Gapmer targeting rat Alivec (AlivecGap). After 48 hours, cells were treated with either 100 nM of Angiotensin II or equivalent volume of 1x PBS for 3 hours. Total RNA was extracted and gene expression analyzed using rat microarrays.

first: Vishnu

last: Samara

first: Vinay

middle: S

last: Tanwar


title: Elaiophylin reduces body weight and lowers glucose levels in obese mice by activating AMPK

city: Shanghai

first: Ruoxuan

last: Bao

address: Dongan road

institute: Fudan University

summary: Obesity is an epidemic affecting 13% of the global population and increasing the risk of many chronic diseases. However, only several drugs are licensed for pharmacological intervention for the treatment of obesity. As a master regulator of metabolism, the therapeutic potential of AMPK is widely recognized and aggressively pursued for the treatment of metabolic diseases. We found that elaiophylin (Ela) rapidly activates AMPK in a panel of cancer cell lines, as well as primary hepatocytes and adipocytes. Meanwhile, Ela inhibits the mTORC1 complex, turning on catabolism and turning off anabolism together with AMPK. In vitro and in vivo studies showed that Ela does not activate AMPK directly; instead, it increases cellular AMP/ATP and ADP/ATP ratios, leading to AMPK phosphorylation in a LKB1-dependent manner. AMPK activation induced by Ela caused changes in diverse metabolic genes, thereby promoting glucose consumption and fatty acid oxidation. Importantly, Ela activates AMPK in mouse liver and adipose tissue. As a consequence, it reduces body weight and blood glucose levels and improves glucose and insulin tolerance in both ob/ob and high fat diet-induced obese mouse models. Our study has identified a novel AMPK activator as a candidate drug for the treatment of obesity and its associated chronic diseases.

overall_design: mRNA profiles of primary hepatocytes with or without Elaiophylin treatment.

first: Hai-xin

last: Yuan

first: Yongjun

last: Dang


title: High-throughput sequencing of the IGH repertoire in human peripheral blood and bone marrow

first: Qing

last: Min

address: 138 Yi Xue Yuan Road

department: Immunology

summary: We applied high-throughput sequencing of the IGH repertoire in peripheral blood and bone marrow (BM) of a primary immunodeficiency patient.  We obtained 325994 IGH sequences from the BM sample and 72597 IGH sequences from the peripheral blood. After comparing with  IMGT/GENE-DB database (http://www.imgt.org), we found obviously increased CDR3 clonality in the patient BM as compared to his peripheral blood. Furthermore, the frequency of IgG transcripts in the patient BM was higher than that in the peripheral blood while the frequency of IgM transcripts was similar.

overall_design: IGH repertoire of peripheral blood and BM in one patient

first: Ji-Yang

last: Wang


title: Transcriptional profiling of Regulatory T cells isolated from ApoE-/- and wild type mice

city: Philadelphia

first: Ying

last: Shao

state: Pennsylvania

address: 3500 N Broad St, MERB1083A

institute: Temple University

summary: Purpose: The goals of this study were to identify preferential gene expression signatures that are unique to Tregs in the development of atherosclerosis.  Methods and results: ApoE-/- and widetype mice were fed with high fat diet for 12 weeks.CD4+Foxp3+ Tregs from spleen were purified by cell sorting (using the Treg GFP reporter mouse line Foxp3/GFP) to generate mRNA transcription profiles. Transcriptional profiling revealed a unique Treg signatures in ApoE-/- mice relative to wildtype mice.  Conclusion: Our study represents the first detailed analysis of splenic Treg transcriptome in atherosclerotic mice.

overall_design: Spleen treg mRNA profiles of ApoE-/- and widetype mice after receiving 12 weeks high fat feeding.

first: Xiaofeng

last: Yang


title: Induction of inverted morphology in brain organoids by vertical-mixing bioreactors

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: Organoid technology provides an opportunity to generate brain-like structures by recapitulating developmental steps in the manner of self-organization. We examined the vertical-mixing effect on brain organoid structures using bioreactors and established inverted brain organoids. The organoids generated by vertical mixing showed neurons that migrated from the outer periphery to the inner core of organoids, in contrast to orbital mixing. To uncover the mechanisms of the inverted structure, we investigated the direction of primary cilia, a cellular mechanosensor. Primary cilia of neural progenitors by vertical mixing were aligned in a multidirectional manner, and those by orbital mixing in a bidirectional manner. Single-cell RNA sequencing revealed that neurons of inverted brain organoids presented a GABAergic character of the ventral forebrain.

overall_design: We conducted single-cell RNA-sequencing to dissect transcriptional traits of the cells in brain organoids.

first: Dang

middle: N

last: Suong

first: Keiko

last: Imamura

first: Ryotaro

last: Kabai

first: Satoko

last: Sakamoto

first: Haruhisa

last: Inoue


title: RNA-sequencing for the characterization of the transcriptome of MCF-7-derived mammospheres and parental breast cancer cells.

city: Ioannina

first: Angeliki

last: Magklara

address: Panepistimioupoli Ioanninon

department: Department of Medicine/Department of Biomedical Research (Ioannina) Foundation for Research & Technology-Hellas

country: Greece

institute: University of Ioannina/nstitute of Molecular Biology & Biotechnology

summary: RNA-sequencing was performed in MCF-7-derived mammospheres and parental breast cancer cells in an effort to identify novel regulators of stemness that could potentially be targeted in luminal ER+ tumors. The bioinformatic analysis identified numerous differentially expressed genes including several known stemness markers, as well as novel genes that may play an important role in breast cancer stem cells.

overall_design: Examination of the transcriptome of MCF-7 derived mammospheres and parental breast cancer cells grown in 2D monolayers  and comparison of their gene expression profiles. The experiment was performed in biological duplicates.

first: John

last: Verigos

first: Styliani

last: Papadaki

first: Dimitris

last: Kordias


title: Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem

city: Buenos Aires

first: Florencia

last: Bannoud

address: Av Rivadavia 1971

country: Argentina

institute: Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)

summary: Purple carrots can accumulate large quantities of anthocyanins in their roots. Depending on the genetic background, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns, confined to the root phloem or xylem tissues. Within the phloem, the tissue usually contributing most of the overall anthocyanin concentration in the carrot root, purple pigmentation can be found in the outer phloem (OP) (also called cortex) and inner phloem (IP) tissues, or it can be confined exclusively to the OP. The latter is a fairly-common phenotype in many purple carrot cultivars. In this work, the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root OP and IP tissues was investigated by means of linkage mapping, transcriptome (RNA-seq), phylogenetic, and gene expression (RT-qPCR) analyses in two genetic backgrounds; an F2 mapping population (3242) and the inbred line B7262. Genetic mapping of the ‘root outer phloem anthocyanin pigmentation’ (ROPAP) and inner phloem pigmentation (RIPAP) revealed co-localization of ROPAP with the P1 and P3 genomic regions previously known to condition pigmentation in different genetic stocks, whereas RIPAP co-localized with P3 only. Transcriptome analysis of purple OP (POP) vs. non-purple IP (NPIP) tissues, along with linkage and phylogenetic data, allowed an initial identification of 28 candidate genes, 19 of which were further evaluated by RT-qPCR in independent root samples of 3242 and B7262, revealing 15 genes consistently upregulated in the POP in both genetic backgrounds, and two genes upregulated in the POP in specific backgrounds. These include seven transcription factors (4 MYBs, 1 bHLH, 1 MADS-box, 1 ERF), seven anthocyanin structural genes, and two genes involved in cellular transport. Altogether, our results point at DcMYB7, DcMYB113, and a MADS-box (DCAR_010757) as the main candidate genes conditioning ROPAP in 3242, whereas DcMYB7 and MADS-box condition RIPAP in this background. In 7262, which roots present purple pigmentation only in the outer phloem, DcMYB113 conditions ROPAP

overall_design: Outer purple phloem and inner non-purple phloem

first: Sofia

last: Carvajal

first: Shelby

last: Ellison

first: Douglas

last: Senalik

first: Sebastian

last: Talquenca

first: Massimo

last: Iorizzo

first: Philipp

last: Simon

first: Pablo

last: Cavagnaro


title: Modulation of global expression by aneuploids and CNV of dosage sensitive regulatory genes

city: Beijing

first: Lin

last: Sun

address: Xinjiekouwai Street

institute: Beijing Normal University

summary: We investigated the effect of pcf11 duplication on gene expression across the transcriptome.

overall_design: Comapare the global expression of pcf11 duplication and wildtype Drosophila.

first: Shuai

last: Zhang


title: Genome-wide identification and expression analysis of MADS-box family genes in litchi (Litchi chinensis Sonn.) and their involvement in floral organogenesis

city: Guangzhou

first: hongling

last: guan

address: tianhe

institute: South China Agricultural University

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Peritoneal metastasis of colorectal cancer (pmCRC): Identification of predictive molecular signatures by a novel preclinical platform of matching pmCRC PDX/PD3D models

city: Berlin

first: Mathias

last: Dahlmann

address: Robert-Rössle-Str. 10

department: Experimental and Clinical Research Center

country: Germany

institute: Charité University Medicine

summary: 14 PDX models of pmCRC were established, including 9 matched PD3D/PDX models, and treatment response to 17 SoC and targeted therapies was monitored, which resulted in drug-dependent inter- and intra-patient specific growth inhibition.  Analysis of the molecular data of the models and patient tissue resulted in the identification of predictive biomarkers for treatment with 5-FU, irinotecan, trametinib, erlotinib, cetuximab and avastin, oxaliplatin, selumetinib, docetaxel and everolimus. Conclusions: The establishment of a preclinical drug testing platform based on in vitro and in vivo matched pmCRC models, molecularly characterized by multi-omics technology, facilitated the identification of predictive biomarkers for treatment response, as well as cancer relevant signatures for effective therapies, ready for validation in clinical cohorts.

overall_design: Transcriptomic analysis of pmCRC patient metastases (n=13), corresponding PDX tumors (n=14) and matching PD3D cell culture models (n=8).

first: Guido

last: Gambara

first: Bernadette

last: Brzezicha


title: Genome-wide identification and expression analysis of MADS-box family genes in litchi (Litchi chinensis Sonn.) and their involvement in floral organogenesis II

summary: Litchi possesses unique ﬂower morphology and adaptive reproduction strategies. Although previous attention has been intensively devoted to the mechanisms underlying its floral induction, the molecular basis of flower organ development remains largely unknown. MADS-box genes are promise candidates for this due to their significant roles in various aspects of inflorescence and flower organogenesis. Here, we present a detailed overview of phylogeny and expression profiles of 101 MADS-box genes that were identified in litchi. These LcMADSs are unevenly located across the 15 chromosomes, and can be divided into type I and type II genes. Fifty type I MADS-box genes are sub-divided into Mα, Mβ and Mγ subgroups, while fifty-one type II LcMADSs consist of 37 MIKCC -type and 14 MIKC*-type genes. Both two types of LcMADS genes mainly contain ABA and MeJA response elements. Tissue-specific and development-related expression analysis reveals that LcMADS51 could be positively involved in litchi carpel formation, while six MADS-box genes including LcMADS42/46/47/75/93/100 play a possible role in stamen development. GA is positively involved in the sex determination of litchi flowers by regulating the expression of LcMADS75 (LcAP1) and LcMADS51 (LcSTK). However, JA probably plays a negative role in litchi flower development.

overall_design: Analysis of MADS-box gene expression at different developmental stages in female and male litchi flowers

first: Houbin

last: Chen

first: Jiyuan

last: Shen

first: Hongling

last: Guan


title: Establishment of a bovine rumen epithelial cell line

city: Blacksburg

first: Honglin

last: Jiang

state: VA

address: 3130 Litton Reaves Hall

department: Animal and Poultry Sciences

institute: Virginia Polytechnic Institute and State University

summary: The goal of this study was to characterize a single-cell clone derived from bovine rumen epithelium. Analyses including RNA-seq demonstrated that this clone was derived from a rumen epithelial cell. This clone is named BREC1 in the manuscript.

overall_design: An RNA-seq library was prepared and sequenced from the clone originally named bREC1P13.


title: LRGASP challenge WTC11 ssCAGE sequencing derived peaks

city: Yokohama

first: Harshita

last: Sharma

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN IMS

summary:
The LRGASP challenge encompasses different human, mouse, and manatee samples sequenced using multiple combinations of protocols and platforms. Different challenges will use distinct subsets of the samples for evaluation. The long-read sequencing platforms used in these challenges are the Pacific Biosciences (PacBio) Sequel II, Oxford Nanopore (ONT) MinION and PromethION. Samples will also be sequenced on the Illumina HiSeq 2500. The primary LRGASP library prep protocols are “standard” cDNA sequencing, direct RNA sequencing, R2C2, and CapTrap. Each sample will also include Lexogen SIRV-Set 4 spike-ins. We will also provide simulated PacBio and ONT data as part of the evaluations.
This particular study focuses on single strand CAGE sequencing of human iPSCs, defining CAGE peaks from Illumina HiSeq 2500 (SR: 150 cycles) of two biological replicates for use in the LRGASP challenge.

overall_design: ssCAGE peak calls of two biological replicates of iPSCs derived from adult skin (leg) fibroblasts

first: Matthew

last: Valentine

first: Kentaro

last: Kaji

first: Hazuki

last: Takahashi

first: Piero

last: Carninci


title: Global analysis of the zinc homeostasis network in Pseudomonas aeruginosa (DOI: 10.3389/fmicb.2021.739988)

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

institute: University of Geneva

summary: In this study we followed up the dynamics of all genes involved in zinc homeostasis in Pseudomonas aeruginosa from starvation to excess, as it happens during infection. The results showed a hierarchical induction of the export systems and a global repression of import mechanisms

overall_design: In this study, three cultures of wild type Pseudomonas aeruginosa, followed up for 60 min after zinc induction, were used to acquire mRNA counts of  25 target genes and 4 reference genes.

first: K

last: Perron

first: V

last: Ducret


title: Transcriptomics analysis and redox-dependent metabolic rewiring in triple-negative breast cancer cells

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

institute: IBSBC CNR

summary: Glucose metabolism toward aerobic glycolysis provides cancer cells with a rapid generation of pyruvate, ATP, and NADH. CtPB2, an NADH-dependent transcriptional co-regulator, has been proposed to work as an NADH sensor, linking metabolism to transcriptional reprogramming. Here we described how the down-regulation of CtBP2 strongly reduces cell proliferation in triple negative breast cancer (BC) cell line, by modulating several intracellular pathways also through gene expression modification. Our data highlight the critical role of NADH in controlling energetic and anabolic demands in cancer cells.

overall_design: In this work, we analyzed as two-color hybridizations using Agilent Technologies whole human genome 4x44K microarrays, the Gene expression profiles (GEP) modification regulated by CtPB2 in MDA-MB-231 breast cancer cell line. Samples were named as follows: shCtBP2 cells (CtBP2 silencing in MDA-MB231 cancer cells by stable RNA interference of CtBP2); HIPP (small CtBP2 inhibitor) and P4 (small CtBP2 inhibitor), all compared to control sample represented by untreated MDA-MB-231 BC cell line.


title: Zinc supplementation with or without additional micronutrients does not affect peripheral blood gene expression or serum cytokine level in Bangladeshi children

city: Parkville

first: Peter

last: Hickey

address: 1G Royal Parade

country: Australia

institute: WEHI

summary: Preventive zinc supplementation provided as a stand-alone dispersible tablet, or via home fortification as multiple micronutrient powders (MNPs), has been considered a potential strategy to prevent zinc deficiency and improve health (including immune) outcomes among children in low- and middle-income countries. However, the impact of zinc supplementation on immune profiles has not been well characterised. We sought to define the effect of zinc supplementation on peripheral blood gene expression  among young children in Dhaka, Bangladesh. In a sub study of a large randomized, controlled, community-based efficacy trial where children 9-11 months of age received one of the following interventions on a daily basis for 24 weeks 1) MNPs containing 10 mg of zinc; 2) dispersible tablet containing 10 mg zinc; or 3) placebo powder, we used RNA-sequencing to profile the peripheral blood gene expression, as well as highly sensitive multiplex assays to detect cytokine profiles. We profiled samples from 100 children enrolled in the parent trial. We did not detect an effect from either zinc intervention on differential peripheral blood gene expression at the end of intervention, or an effect from intervention on change in gene expression from baseline. We also did not detect an effect from either intervention on cytokine concentrations. Exploratory analysis did not identify an association between undernutrition (defined as stunting, underweight or wasting) on peripheral blood gene expression.

overall_design: Peripheral blood mRNA profliing in children pre- and post- 6 months intervention (zinc tablet, micronutrient powder containing zinc, or placebo) as part of a randomised controlled trial.

first: Sant-Rayn

last: Pasricha


title: Photoactivatable senolysis with single-cell resolution reverses aging

first: Donglei

last: Shi

address: meilong road 130

institute: Science and technology of east China university

summary: Cellular senescence is a crucial biological process associated with pathologies of aging. The elimination of senescent cells (SnCs) for the purpose to extend healthy lifespan has been supported by emerging evidence, which causes the exploration of drug approaches to induce SnCs death (senolysis). The challenge then becomes how to achieve the precision, broad-spectrum and controllability of senolysis. To this end, we here propose an unprecedented integration strategy to design a senotherapeutic agent

overall_design: Examination of control group, doxo group and doxo-KSL0608-Se group in liver of mice by RNA-seq, in quadruplicate

first: Wenwen

last: Liu

first: Ying

last: Gao

first: Yuan

last: Guo

first: Jian

last: Li


title: Characterization of the Radiation Desiccation Response regulon of the radioresistant bacterium Deinococcus radiodurans by integrative genomic analyses.

city: Gif sur Yvette

first: Fabrice

last: Confalonieri

address: Avenue de la Terrasse

department: Genome Biology

institute: Institute for Integrative Biology of the Cell (I2BC)

summary: In this study, we mapped the DdrO regulon in Deinococcus radiodurans by using two genome-scale approaches, ChIP-seq and RNA-seq analyses. These approaches were performed to find additional DdrO targets sites that were not predicted by previous in silico analyses. To our knowledge, we present here the first ChIP-seq analysis performed at the genome level in D. radiodurans. Alignments of DNA sequences extracted from ChIP-seq analysis were also performed to compare the consensus motif found to the predicted DdrO-binding motif.  Our results show that the RDR regulon in D. radiodurans is more complex than previously thought and is composed of at least 35 genes, including such DNA and RNA metabolism proteins as RecG and HelD helicases, and the prokaryotic replicative DNA ligase LigA, but also new genes associated with different metabolic pathways, involved in translation or encoding proteins of unknown function.

sample_organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

overall_design: For RNA-seq: 12 RNAseq samples with 3 replicates each separated between two experiments.Two time course experiments using ΔddrO strains complemented by ddrO expressed, under its own promoter, from a plasmid with wild type or thermosensitive replication.  For ChIP-seq: 3 ChIP-seq samples with 3 replicates for IP samples, one replicate for Input sample and  one replicate for Mock sample.

first: Nicolas

last: Eugénie

first: Yvan

last: Zivanovic

first: Gaelle

last: Lelandais

first: Geneviève

last: Coste

first: Claire

last: Bouthier de la Tour

first: Esma

last: Bentchikou

first: Pascale

last: Servant


title: Repositioning of  a GABA-B receptor agonist, AZD3355 (Lesogaberan), for the treatment of Non-Alcoholic Steatohepatitis

city: New York

first: Christine

last: Becker

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: Non-alcoholic steatohepatitis (NASH) is a rising health challenge, with no approved drugs.   We used a computational drug repositioning strategy to uncover a novel therapy for NASH, identifying a GABA-B receptor agonist, AZD3355 (lesogaberan) previously evaluated as a therapy for esophageal reflux.  AZD3355’s potential efficacy in NASH was tested in human stellate cells.  Transcriptomic analysis of these responses identified key regulatory nodes impacted by AZD3355.

overall_design: To investigate the effects of AZD3355 we treated primary human hepatic stellate cells with 30 nM of AZD3355 for 72 hours and then performed transcriptomic analysis.

first: Dipankar

last: Bhattacharya

first: Jacqueline

last: Novik

first: Joel

last: Dudley

first: Scott

middle: L

last: Friedman


title: SMTNL1 Regulates Development and Metabolic Transformation of Skeletal Muscle in Hyperthyroidism

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary:
Aim. Hyperthyroidism reduces the oxidative capacity of skeletal muscle (SKM) and promotes development of a glycolytic phenotype by altering the expression of metabolic proteins. Our previous results showed that smoothelin-like protein 1 (SMTNL1), a transcriptional coregulator, promotes insulin sensitivity in SKM.  Our aim was to elucidate the role of SMTNL1 in SKM under physiological and pathological 3,3′,5-Triiodo-L-thyronine (T3) concentrations.  Methods. Human hyper- and euthyroid SKM biopsies were used for microarray analysis and phospho-kinase arrays. Physiological and hyperthyroid concentrations of T3 were applied on differentiated C2C12 cells upon SMTNL1 overexpression to assess the activity and expression level of the element of insulin signaling. Real-time metabolic measurements of oxygen consumption rate and extracellular acidification rate were measured.    Results. Expression of genes related to energy production, nucleic acid- and lipid metabolism were changed significantly in hyperthyroid samples. SMTNL1 expression decreased in the hyperthyroid samples and in T3 treated C2C12 cells. SMTNL1 regulated muscle cell differentiation and compensated for the glycolytic shift in SKM triggered by pathological T3 exposure. Moreover, it selectively regulated TR expression at the transcriptional level. T3 excess triggered the development of insulin resistance while overexpression of SMTNL1 induced insulin sensitivity through the inhibition of JNK activity and hampered the non-genomic effects of T3 by decreasing the activity of ERK1/2 through PKC. SMTNL1 overexpression induced GLUT4 expression in hyperthyroid model to restore the normal responsiveness of glucose transport to insulin. SMTNL1 regulated glucose phosphorylation and balances glycolysis and glycogen synthesis via the downregulation of hexokinase II. T3 overload strongly increased the rate of lactate production, while SMTNL1 overexpression antagonizes the T3 effects.  Conclusion. These lines of evidence suggest that SMTNL1 potentially prevents hyperthyroidism-induced changes in SKM and it holds great promise as a novel therapeutic target.
Smoothelin-like Protein 1 in Hyperthyroidism

overall_design: Human sternohyoid muscle biopsies from euthyroid (eu) and hyperthyroid (hyper) donors (n=3) were homogenized in Trizol and RNA were extracted.

first: Evelin

last: Major

first: Ferenc

last: Győry

first: Dániel

last: Horváth

first: István

last: Tamás

first: Ilka

last: Keller

first: Karen

last: Uray

first: Péter

last: Fülöp

first: Beáta

last: Lontay


title: RNA sequencing of human endometrial epithelial and stromal cell lines treated with AG-205

city: Brussels

first: Patrick

last: Henriet

address: Avenue Hippocrate, 75

department: De Duve Institute

country: Belgium

institute: Université Catholique de Louvain

summary: Inappropriate response to progesterone or synthetic progestogens by the endometrial tissue may penalize the efficiency of treatments against endometriosis. The response pathways to progesterone involve its nuclear receptor but alternative mechanisms seem to play complementary roles. Recent studies have shown that Progesterone Receptor Membrane Component-1 (PGRMC1) can control various physiological or pathological processes in the breast and ovary. However, its functions in the human endometrium remain largely unknown. The small compound AG-205 is an alleged specific inhibitor of PGRMC1. Transcriptomes were obtained by RNA sequencing from cells of two endometrial cell lines (HEC-1A of epithelial origin and T-HESC of fibroblast origin) cultured in the presence or not of AG-205.

overall_design: Comparaison of mRNA profiles of epithelial or stromal endometrial cells treated with 15µM or DMSO control for 32h

first: Charlotte

last: Thieffry

first: Marie

last: Van Wynendaele

first: Axelle

last: Loriot


title: Suceptibility of non target crustacean Eurytemora affinis  to endocrine disruptor tebufenozide: a transcriptomic approach

city: Le Havre

first: Caroline

last: Arcanjo

address: 25, rue Philippe Lebon

institute: UMR-I02 SEBIO

summary: Copepods are zooplanktonic crustaceans ubiquitously widespread in aquatic systems. They are of ecological importance due to their place in the trophic chain. Copepods are exposed to a wide variety of pollutants as insect growth regulators (IGR) acting as endocrine disruptors although they are not the target. The aim of the present work was to investigate the molecular response of a non-targeted organism, the copepod Eurytemora affinis, to an IGR. Adult males and females were exposed at two sub-lethal concentrations of tebufenozide (TEB), an agonist of the ecdysone receptor targeting lepidopteran larvae. Results suggest a gender-specific response with a higher sensitivity in males potentially due to a differential activation of stress response pathways. Indeed, genes coding for proteins involved in stress response were mis-regulated in males while not in females suggesting that detoxification processes are still ongoing in males. In both genders, TEB exposure triggers similar pathways as for its targeted species by modulating the transcription of early and late ecdysone responsive genes. Among them, genes involved in cuticle metabolism, muscle contraction, neurotransmission and gametogenesis whose mis-regulation could lead to moult, locomotor and reproductive impairments. Furthermore, genes coding for proteins playing part in epigenetic processes were found in both genders highlighting the potential impact of TEB exposure on further generations. Beyond the in-depth knowledge of the molecular MoA of an ecdysone agonist on a non-targeted organism, this work provides data allowing the identification of (i) potential biomarkers of ecdysone agonists and (ii) putative physiological responses to be further assessed to characterize the effects of TEB at higher biological levels. The present study reinforces the suitability of the use E. affinis as an ecotoxicological model.

overall_design: RNAseq analysis of adult males and females copepods Eurytemora affinis exposed to 0,5 µg/L and 50 µg/L of tebufenozide or non-exposed controls. All treatments were made in triplicates.

first: Céline

last: Boulangé-Lecomte


title: Global Histone H3 lysine 4 trimethylation (H3K4me3) landscape changes in response to TGF-β1

city: Ahmedabad

first: Noopur

last: Thakur

state: Gujarat

address: Navrangpura

department: Biological and Life Sciences

country: India

institute: Ahmedabad University

summary: We performed Chromatin-Immunoprecipitation followed by Next-Generation Sequencing (ChIP-Seq) in PC-3 Cells stimulated with TGF-β1  for different duration. We used anti-H3K4me3 antibody to immunoprecipitate DNA fragment associated with H3K4me3. We found that a number of regions associated with H3K4me3  increased in a time-dependent manner upon  TGF-β1 stimulation. Further the regions were classified into different Functional annotations.

overall_design: TGF-β play a critical role in Epithelial to Mesenchymal Transition (EMT) in different types of cancers. TGF- β can exhibit pro and anti-tumour activities in cancer cells in a context and microenvironment dependent manner. On the hand epigenetic modifications are increasingly playing an important role in various cellular processes. Aberration in epigenetic processes can lead to disruption in different gene functions and malignant cellular transformation. There is a growing interest in understanding the role of H3K4me3 in cancer survival. Investigation on the epigenetic reprogramming during the TGF- β induced EMT, found a global reduction in the heterochromatin mark H3 Lys9 dimethylation (H3K9me2), an increase in the euchromatin mark H3 Lys4 trimethylation (H3K4me3) and an increase in the transcriptional mark H3 Lys36 trimethylation (H3K36me3). As TGF-β and H3K4me3 plays an important role in tumorigenesis, our study focuses on finding globally, H3K4me3 associated regions in response to TGF-β. ChIP-Seq was performed in Prostate cancer cells (PC-3) to understand the involvement and mechanism of H3K4me3 modification in TGF-β induced EMT.

first: Ankit

last: Naik


title: A transcriptional and open chromatin landscape and the role of ONECUT1 in  human pancreas differentiation [RNA-seq]

city: Aachen

first: Ivan

last: Costa

address: Pauwelsstraße 19

institute: Unikilink RWTH Aachen

summary: Pancreatic differentiation and specification of lineages is a tightly controlled process involving a interconnected network of transcriptional regulation. Although more knowledge on human pancreatic development is accumulating, the precise role of many transcription factors is only described in mouse. Therefore, it is of great interest to expand our knowledge using alternative model systems such as pancreatic in vitro differentiation of human pluripotent stem cells. Here, we provide stage-specific data from RNA-, ChIP-, and ATAC-sequencing to dissect transcriptional and regulatory mechanisms during pancreatic development. Transcriptome and open chromatin maps of pancreas differentiation from human pluripotent stem cells provide a stage-specific pattern of known pancreas transcription factors and determine ONECUT1 as a crucial regulator in pancreas progenitors. Moreover, our data suggest that ONECUT1 is also involved in preparing pancreatic progenitors for later endocrine specification.Our approach of dissecting the transcriptional and regulatory mechanisms revealed an important role for the specific key player ONECUT1 and will help to better understand human development and disease.

overall_design: The human embryonic stem cell line HUES8 differentiated to definitive endoderm, pancreatic endoderm and pancreatic progenitor cells was used for RNA sequencing.

first: Zhijian

last: Li

first: Alexander

last: Kleger

first: Sandra

last: Heller


title: RNA-Seq of mice Bone Marrow Mononuclear Cells (BMMCs) under IL-3 +  IL-33 or Dexamethasone (Dex) or  transforming growth factor beta-1 (TGFb) tretament

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: Comparison of gene expression after treatment of mice Bone Marrow Mononuclear Cells (BMMCs) with either IL-3 or IL-3+IL-33 or IL-3+Dex or IL-3+TGFb.

overall_design: 12 samples in four groups: IL-3: 3 samples, IL-3+IL-33: 3 samples, IL-3+Dex: 3 samples, IL-3+TGFb: 3 samples

first: Nico

last: Andreas

first: Sebastian

last: Drube


title: Gene expression signature of ex vivo expanded NK cells for 14 days

city: Seongnam-si

first: Daun

last: Jung

state: Gyeonggi-do

address: Bundang-gu, 삼평동 689

department: Department of Pathology

institute: CHA Bundang Medical Center

summary: we performed RNA sequencing to employ an unbiased approach to identify the altered gene expression enhancing the function of ex vivo expanded pNK cells for 14 days, and transcriptionally compared day 0 and day 14 pNK cells.

overall_design: mRNA profiles of day0 PBMC and expanded NK for 14 days

first: Yonugseok

last: Baek


title: Targeting netrin-1 in established atherosclerosis promotes inflammation resolution and plaque regression

first: Emily

last: Brown

address: 435 E 30th St

department: Medicine

institute: NYU Langone

summary: We used single cell RNA-sequencing of aortic CD45+ leukocytes, combined with immunohistologic, morphometric and flow cytometric analyses to define the changes in plaque immune cell composition and to define the immunological landscpape changes following the deletion of netrin-1

overall_design:
CD45+ aortic leukcytes from four conditions:
baseline of pooled WT CD45+ aortic leukocytes
baseline of pooled Ntn1 CD45+ aortic leukocytes, prior to deletion of netrin-1
regression of pooled CD45+ aortic leukocytes with netrin-1
regression of pooled CD45+ aortic leukocytes after deletion of netrin-1

first: Katrhryn

middle: J

last: Moore

first: Martin

last: Schlegel

first: Monika

last: Sharma

first: Milessa

last: Afonso

first: Emma

last: Corr

first: Graeme

last: Koelwyn

first: Coen

last: van Solingen

first: Alexandra

last: Newmann

first: Yannick

last: Cyr

first: Lianne

last: Shanley

first: Daniel

last: Peled

first: Ann

last: Schmidt

first: Edward

last: Fisher


title: CRISPR/Cas9/AAV9-sgRNA Mediated In Vivo Genome Editing  Reveals the Indispensability of Myc During Muscle Stem Cells Activation by Remodeling the 3D Chromatin [DEEP-seq(MyoD&Myc&Bcl6&Pknox2)]

city: Hong Kong

first: Yingzhe

last: Ding

state: Shatin NT.

address: Rm503,Li Ka Shing Medical Science Build.,Prince of Wales Hosp.,30-32 Ngan SHing St.

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Skeletal muscle satellite cells (SCs) are muscle stem cells responsible for muscle development and injury induced muscle regeneration. The pace of SC related study, however, is constrained partially by the technological limitations in generating genetically modified mice. Although the ease of use of CRISPR-Cas9 in genome manipulation has been documented in many cell lines and various species, its application in endogenous SCs remains elusive. In this study, we generated muscle-specific Cas9-expressing mice and achieved robust in vivo genome editing in juvenile SCs at the postnatal stage through AAV9 mediated short guide RNAs (sgRNAs) delivery. We also found adult quiescent SCs are reluctant to CRISPR/Cas9 editing despite efficient AAV9 transduction. To edit juvenile SCs in vivo, as a proof-of-concept, we delivered sgRNAs targeting MyoD, a key gene critical for muscle physiology and showed an efficient editing at MyoD locus, resulting in accumulation of SCs and defects in SCs differentiation which resembled the phenotypes reported in MyoD knockout mice. Further application of this system on potential key transcription factors (TFs) involved in SC fate transition, Myc, Bcl6 and Pknox2, unveiled their distinct functions in the early stage of SC activation and injury induced muscle regeneration. In addition, we revealed that Myc orchestrated SCs activation through impinging on 3D chromatin architecture. Altogether we established a robust muscle restricted CRISPR/Cas9-based gene editing platform in endogenous SCs and elucidated the functionality of key factors governing SC activities.

overall_design: a middle dose (1×1011 vg/mouse) of single AAV9-dual sgMyoD, sgMyc,sgPknox2 or sgBcl6 virus was injected into Pax7Cas9 mice intramuscularly at P10.Muscle stem cells were isolated 4 weeks after injection and sgMyoD, sgMyc,sgPknox2 or sgBcl6 targeted locus was amplified from genomic DNA in freshly isolated satellite cells and subjected to deep sequencing.

first: Wang

last: Huating

first: Sun

last: Hao

first: He

last: Liangqiang

first: Ding

last: Yingzhe

first: Qiang

last: Sun


title: A transcriptional and open chromatin landscape and the role of ONECUT1 in human pancreas differentiation

first: Ivan

last: Costa

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Gene expression signature of ex vivo expanded NK(CD3-CD56+) cells for 14 days

first: Daun

last: Jung

summary: We performed RNA sequencing to employ an unbiased approach to identify the altered gene expression enhancing the function of ex vivo expanded pNK cells for 14 days, and transcriptionally compared day 0 and day 14 pNK cells.

overall_design: mRNA profiles of sorted day0 NK(CD3-CD56+) and expanded NK(CD3-CD56+) for 14 days

first: Yonugseok

last: Baek


title: CRISPR/Cas9/AAV9-sgRNA Mediated In Vivo Genome Editing  Reveals the Indispensability of Myc During Muscle Stem Cells Activation by Remodeling the 3D Chromatin [Hi-C]

overall_design: The in situ Hi-C libraries were prepared as previously reported. Briefly, isolated SCs were digested using 100U DpnII overnight at 37 °C and then filled in with biotin for 1.5 hours at 37 °C; ligated for 4.5 hours at room temperature. DNA was purified by ethanol precipitation, and then sheared into 300-400bp fragments using Covaris S220. DNA fragments containing biotin were enriched by Dynabeads MyOne Streptavidin C1 (Invitrogen 65001) for 15min at room temperature, followed by end repairing, adaptor ligation and PCR amplification as described. At least two biological replicates were performed for both control and sgMyc groups. The libraries were then sequenced via the Illumina HiSeq X Ten system at Genewiz company.

first: Zhao

last: Yu


title: Inhibition of the multifunctional homeodomain-interacting protein kinase 2 (HIPK2) alleviates thoracic aortic disease in mice with progressively severe Marfan syndrome

first: Jens

last: Hansen

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

summary: Thoracic aortic aneurysm (TAAs) are a severe complication in Marfan Symdrome (MFS), often leading to dissection and premature death. To identify potential drug targets for the treatment for TAAs we used gene expression profiles from MFS mice and patients to predict kinases that regulate gene expression. Among the top predictions was the kinase HIPK2. Ubiquitous post-natal inactivation of the HIPK2 gene, as well as chronic administration of an allosteric inhibitor of HIPK2/Smad3 interaction, increased the survival of MFS mice and improved multiple surrogate parameters.

overall_design: The data that was first published with this study, contained 4 samples obtained from both MFS and WT mice and 3 samples obtained from both MFS patients and non-MFS control subjects.

first: Cristina

middle: I

last: Caescu

first: Wenzhen

last: Xiao

first: Pauline

last: Arnaud

first: Bart

last: Spronck

first: Takeshi

last: Hashimoto

first: Sae-Il

last: Murtada

first: Roshan

last: Borkar

first: Jay

middle: D

last: Humphrey

first: James

last: Gallo

first: Guillaume

last: Jondeau

first: Catherine

last: Boileau

first: Ravi

last: Iyengar

first: John

last: He

first: Francesco

last: Ramirez


title: CRISPR/Cas9-mediated knockout of PIM3 suppresses tumorigenesis and cancer cell stemness in human hepatoblastoma cells.

city: Birmingham

first: Elizabeth

last: Beierle

state: AL

address: 1670 University Blvd

institute: University of Alabama at Birmingham

summary: Hepatoblastoma remains one of the most difficult childhood tumors to treat and is alarmingly understudied. Over half of patients initially present with locally advanced or metastatic disease and the prognosis for this cohort remains dismal. In addition, many of these children have disease that is resistant to standard therapies and will require novel and targeted therapies to effectively treat or manage their disease. We previously demonstrated that Proviral Insertion site in Maloney murine leukemia virus (PIM) kinases, specifically PIM3, are overexpressed in human hepatoblastoma cells and function to promote tumorigenesis. We aimed to use CRISPR/Cas9 gene editing technology with dual gRNAs to introduce large inactivating deletions in the PIM3 gene and achieve stable PIM3 knockout (KO) in the human hepatoblastoma cell line, HuH6. PIM3 KO of hepatoblastoma cells led to significantly decreased proliferation, viability, and motility, inhibited cell-cycle progression, decreased tumor growth in a xenograft murine model, and increased animal survival. Analysis of RNA sequencing data revealed that PIM3 KO downregulated expression of pro-migratory and pro-invasive genes and upregulated expression of genes involved in apoptosis and differentiation. Furthermore, PIM3 KO decreased hepatoblastoma cancer cell stemness as evidenced by decreased tumorsphere formation, decreased mRNA abundance of stemness markers, and decreased cell surface expression of CD133, a marker of hepatoblastoma stem cell-like cancer cells. Reintroduction of PIM3 into PIM3 KO cells rescued the malignant phenotype. These findings emphasize the role of PIM3 in promoting hepatoblastoma tumorigenesis and provide evidence that targeting PIM3 may offer a novel therapeutic approach for children with hepatoblastoma.

overall_design: RNA sequencing of HuH6 WT and PIM3 KO human hepatoblastoma cells.

first: Raoud

last: Marayati

first: Laura

last: Stafman


title: CRISPR/Cas9/AAV9-sgRNA Mediated In Vivo Genome Editing  Reveals the Indispensability of Myc During Muscle Stem Cells Activation by Remodeling the 3D Chromatin [Deep-seq(single vs dual)]

first: Yingzhe

last: Ding

overall_design: To compare the editing efficiency between the single and dual sgRNAs treatment, a middle dose (1×1011 vg/mouse) of single AAV-sgMyoD or AAV9-dual sgMyoD virus was injected into Pax7Cas9 mice intramuscularly at P10 and administration of a middle dose of AAV9 virus containing pAAV9-sgRNA backbone without any sgRNA insertion was used as control. Muscle stem cells were isolated 4 weeks after injection and sgMyoD targeted locus was amplified from genomic DNA in freshly isolated satellite cells and subjected to deep sequencing.

first: Wang

last: Huating

first: Sun

last: Hao

first: He

last: Liangqiang

first: Ding

last: Yingzhe


title: Transcriptome-wide survey of Runx1-interacting RNAs by RNA immunoprecipitation sequencing

city: Bonston

first: Bon

middle: Quy

last: Trinh

state: MA

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

summary: Runt-related transcription factor 1 (RUNX1) plays critical roles in hematopoiesis including myeloid development. Runx1 binds Runt consensus motifs at promoters and regulatory elements of its target genes. Interestingly, several Runx1-binding RNA aptamers have been successfully developed. Additionally, mounting evidences suggest that transcription factors are capable of binding to RNAs. In this study, we performed a transcriptome-wide screen for Runx1-interacting RNAs in living cells using fRIP-Seq. Anti-Runx1 antibody was used to capture Runx1 in the monocytic cell line THP-1. RNAs co-immunoprecipitated with Runx1 were sequenced by paired-end massively parallel sequencing and analyzed by HOMER peak calling and annotation algorithms. By doing so, we identified a repertoire of RNAs interacting with Runx1. We further investigate functional role of these interactions in Runx1-mediated transcription regulation.

overall_design: THP-1 cells, anti-Runx1 antibody,IgG  and Input samples

middle: Q

first: Rory

last: Coffey

first: Mahmoud

last: Basssal

first: Daniel

last: Tenen


title: In vitro pancreas differentiation of human pluripotent stem cell line Mel1.

first: Ivan

last: Costa

summary: We have identified an essential transcription factor for endocrine pancreatic development, that binds to and possibly regulates other isletogenesis transcription factors, driving endocrine differentiation.

overall_design: The human embryonic stem cell line Mel1 differentiated to definitive endoderm, pancreatic endoderm and pancreatic progenitor cells was used for RNA sequencing.

first: Gino

last: Kwon

first: Zhijian

last: Li

first: Alexander

last: Kleger

first: Sandra

last: Heller

first: Ronan

last: Russel

first: Gopika

last: Nair


title: CRISPR/Cas9/AAV9-sgRNA Mediated In Vivo Genome Editing  Reveals the Indispensability of Myc During Muscle Stem Cells Activation by Remodeling the 3D Chromatin [RNA-seq(FISC-DSC)]

overall_design: RNA-seq was performed in freshly isolated or cultured muscle stem cells.

first: Li

last: Yuying


title: The role of FGF21 in the effects of low protein diet on the transcriptome of aged mouse kidneys

city: Baton Rouge

first: Thomas

middle: W

last: Gettys

state: LA

address: 6400 Perkins Road

department: Nutrient Sensing and Adipocyte Signaling

institute: Pennington Biomedical Research Center

summary: FGF21 is a circulating hormone that is required for metabolic responces and transcriptional changes to protein restriction.  In the current study, we observed increased fibrosis and macrophages inflitration into kidney of FGF21 KO mice fed a LP diet compared to NP diet-fed animals, which is not observed in WT mice. The RNAseq experiment was conducted to compare the effect of LP in WT and FGF21 KO mice on renal transcriptome.

overall_design: Comparison of the effect of  low protein (LP) on kidney transcriptome in either WT (each 6 samples from NP and LP fed mice) or FGF21 KO mice (each 6 samples from NP and LP fed mice). Normal protein (NP) contain 20% protein, LP contain 5% protein

first: Han

last: Fang

first: Krisztian

last: Stadler

first: Cristal

last: Hill

first: Christopher

last: Morrison

first: Kirsten

last: Stone

first: Landon

last: Sims

first: Jasleen

last: Kaur

first: Richard

middle: P

last: Carmouche

first: Sara

middle: M

last: Webb

first: Sujoy

last: Ghosh


title: RNA-seq of untreated and IMQ treated mouse back skin in control and Ovol1 deficient mice

city: Irvine

first: Lupe

last: Gutierrez

state: CA

address: 825 Health Sciences Rd D288

institute: University of California, Irvine

summary: Skin constitutes the outer permeability barrier that protects the body from dehydration and a myriad of external assaults. Epidermal keratinocytes act as the first line of innate immune defense, and barrier defects underlie common inflammatory skin diseases. However, the molecular mechanisms that maintain barrier integrity when skin is under challenge to regulate the interplay between epidermal and immune cells are not fully understood. Here we report upregulated expression of transcriptional repressorencoding Ovol1 in epidermal cells of inflamed skin, and its functional importance in maintaining barrier integrity of physically or chemically challenged skin. Following stimulation with imiquimod, Ovol1-deficient mice exhibit significantly aggravated epidermal hyperplasia and psoriasis-like skin inflammation featuring persistent neutrophil accumulation. Using bulk and single-cell RNA-sequencing, we characterize molecular changes in epidermal, fibroblasts, and immune cells that reflect altered epidermal proliferation and differentiation and/or significantly enhanced inflammatory responses as consequences of Ovol1 deletion. We identify both proliferation/differentiation-regulating and neutrophil-attracting chemokine genes as candidate direct targets of Ovol1. Finally, we provide evidence for altered IL-1a signaling in the microenvironment of Ovol1- deficient inflamed skin that functionally contributes to neutrophil accumulation and epidermal hyperplasia. Collectively, our study demonstrates a protective role for an epidermally expressed, disease-linked transcription factor in coordinating robust barrier maintenance with suppression of skin inflammation.

overall_design: RNA-seq of four untreated and four IMQ treated mouse back skin samples in control and Ovol1 deficient mice. Replicates consist of males and females.

first: Xing

last: Dai

first: Peng

last: Sun

first: Remy

last: Vu

first: Guadalupe


title: CRISPR/Cas9/AAV9-sgRNA Mediated In Vivo Genome Editing  Reveals the Indispensability of Myc During Muscle Stem Cells Activation by Remodeling the 3D Chromatin [Deep-seq(dose)]

first: Yingzhe

last: Ding

overall_design: Pax7Cas9 mice were administrated with different doses of single AAV-sgMyoD (high: 5×1011 vg/mouse; middle; 1×1011 vg/mouse; low: 0.2×1011 vg/mouse) virus intramuscularly at P10. Pax7Cas9 mice administrated with a high (5×1011 vg/mouse) dose of AAV9 virus containing pAAV9-sgRNA backbone without any sgRNA insertion were used as control. Muscle stem cells were isolated 4 weeks after injection and sgMyoD targeted locus was amplified from genomic DNA in freshly isolated satellite cells and subjected to deep sequencing.

first: Wang

last: Huating

first: Sun

last: Hao

first: He

last: Liangqiang

first: Ding

last: Yingzhe


title: Role of transcription factor ONECUT1 during in vitro pancreatic differentiation of human pluripotent stem cells

first: Ivan

last: Costa


title: Cytokine Signaling Co-opts the CREB/CRTC Pathway in Obesity

city: San Diego

first: Ezra

last: Wiater

address: 10010 N Torrey Pines Rd

department: PBL

institute: Salk Institute For Biological Studies

summary: Cooperative effects of CREB and NF-kB Pathways on Adipose Tissue Inflammation in Obesity

overall_design: epididymal WAT from normal chow or 15wks high fat diet fed mice and WT_IgG or CRTC2/3 dAKO_IgG or WT_CXCL1/2 neutralizing Ab injected mice under 9wks high fat feeding

first: Young-Sil

last: Yoon

first: Marc

last: Montminy


title: The lysine demethylase KDM4A controls the cell-cycle expression of replicative canonical histone genes

city: Boston

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

summary: Chromatin modulation provides a key checkpoint for controlling cell cycle regulated gene networks. The replicative canonical histone genes are one such gene family under tight regulation during cell division.  These genes are most highly expressed during S phase when histones are needed to chromatinize the new DNA template.  While this fact has been known for a while, limited knowledge exists about the specific chromatin regulators controlling their temporal expression during cell cycle.  Since histones and their associated mutations are emerging as major players in diseases such as cancer, identifying the chromatin factors modulating their expression is critical.  The histone lysine tri-demethylase KDM4A is regulated over cell cycle and plays a direct role in DNA replication timing, site-specific rereplication, and DNA amplifications during S phase.  Here, we establish an unappreciated role for the catalytically active KDM4A in directly regulating canonical replicative histone gene networks during cell cycle.  Of interest, we further demonstrate that KDM4A interacts with proteins controlling histone expression and RNA processing. Together, this study provides a new function for KDM4A in modulating canonical histone gene expression.

overall_design: RNA sequencing of RPE control and stably overexpressing KDM4A sorted based on DNA content in four phases: G1, early S, late S and G2/M

first: Capucine

last: Van Rechem

first: Ruslan

last: Sadreyev

first: Johnathan

middle: R

last: Whetstine


title: CRISPR/Cas9/AAV9-sgRNA Mediated In Vivo Genome Editing  Reveals the Indispensability of Myc During Muscle Stem Cells Activation by Remodeling the 3D Chromatin [RNA-seq (myc&bcl6)]

overall_design: RNA-seq was performed in cultured muscle stem cells isoalted from Pax7cas9 mice infected with AAV9-dual sgMyc/sgBcl6 virus.


title: Antigen-specific type 1 regulatory T cells have a distinct molecular identity and suppress through CTLA-4 and PD-1

city: Stanford

first: Pauline

last: Chen

address: 265 Campus Drive

department: Pediatrics

institute: Stanford University

summary: We report the bulk-cell-based TCR sequences profiling from high-throughput sequencing of human healthy T-allo10 cells. The T-allo10 cell product is consistently enriched for Tr1 cells, is specifically anergic, and suppresses alloantigen-responsive Teff cells. Analysis of Tr1 cells from the T-allo10 product showed that the both TCRa and TCRb repertoires are highly skewed towards dominant clones and has diverged from the parental CD4+ T cells used to generate the T-allo10 product, non-Tr1 cells from the same T-allo10 product, and Teff cells from the control T-allo product. The data indicate that T-allo10-derived Tr1 cells, but not non-Tr1 cells, undergo clonal expansion in response to the alloantigen stimulation, suggesting that the Tr1 cells are the antigen specific component of the T-allo10 cell product. T-allo10 cells are currently undergoing clinical evaluation for safety in a phase I clinical trial (ClinicalTrials.gov ID: NCT03198234).

overall_design: To determine if CD49b+LAG3+ Tr1 or non-Tr1 cells from the total T-allo10 cell product undergo clonal expansion during co-culture with DC-10, we sequenced the TCR repertoires of total T-allo10, sorted Tr1 and non-Tr1 cells from the T-allo10 cells, parental CD4+ T and total control T-allo Teff cells by Illumina Miseq for pair-ended 2x250 or 2x300 sequencing runs.

first: Alma

last: Cepika

first: Rosa

last: Bacchetta

first: Maria

last: Roncarolo


title: Biology of Renal Carcinoma using a Mouse RCC model

city: Pessac Cedex

first: Justine

last: Rudewicz

address: Allée Geoffroy Saint Hilaire Bâtiment B2, Rez-de-Chaussée

department: SVS

institute: University of Bordeaux

type: Methylation profiling by high throughput sequencing

summary: The mouse renal cancer cell line RENCA was serially passaged in vivo using multiple implantation strategies (called Kidney, Tail and Lung) designed to replicate different aspects of primary tumour growth and metastasis. We have acquired methylomic data.

overall_design: MethylSeq data from parental cell line (RENCA), 3 Kidney experiments, 3 Tail experiments and 3 Lung experiments

first: Andreas

last: Bikfalvi